The roles of nuclear orphan receptor NR2F6 in anti-viral innate immunity.

Proper transcription regulation by key transcription factors, such as IRF3, is critical for anti-viral defense. Dynamics of enhancer activity play important roles in many biological processes, and epigenomic analysis is used to determine the involved enhancers and transcription factors. To determine new transcription factors in anti-DNA-virus response, we have performed H3K27ac ChIP-Seq and identified three transcription factors, NR2F6, MEF2D and MAFF, in promoting HSV-1 replication. NR2F6 promotes HSV-1 replication and gene expression in vitro and in vivo, but not dependent on cGAS/STING pathway. NR2F6 binds to the promoter of MAP3K5 and activates AP-1/c-Jun pathway, which is critical for DNA virus replication. On the other hand, NR2F6 is transcriptionally repressed by c-Jun and forms a negative feedback loop. Meanwhile, cGAS/STING innate immunity signaling represses NR2F6 through STAT3. Taken together, we have identified new transcription factors and revealed the underlying mechanisms involved in the network between DNA viruses and host cells.

Slide-free clinical imaging of melanin with absolute quantities using label-free third-harmonic-generation enhancement-ratio microscopy.

The capability to image the 3D distribution of melanin in human skin in vivo with absolute quantities and microscopic details will not only enable noninvasive histopathological diagnosis of melanin-related cutaneous disorders, but also make long term treatment assessment possible. In this paper, we demonstrate clinical in vivo imaging of the melanin distribution in human skin with absolute quantities on mass density and with microscopic details by using label-free third-harmonic-generation (THG) enhancement-ratio microscopy. As the dominant absorber in skin, melanin provides the strongest THG nonlinearity in human skin due to resonance enhancement. We show that the THG-enhancement-ratio (erTHG) parameter can be calibrated in vivo and can indicate the melanin mass density. With an unprecedented clinical imaging resolution, our study revealed erTHG-microscopy's unique capability for long-term treatment assessment and direct clinical observation of melanin's micro-distribution to shed light into the unknown pathway and regulation mechanism of melanosome transfer and translocation.

Comparative analysis of intrinsic skin aging between Caucasian and Asian subjects by slide-free in vivo harmonic generation microscopy.

Phenotypical and functional differences in the intrinsic skin aging process of individuals between Caucasians and Asians have generated considerable interest in dermatology and cosmetic industry. Most of the studies focused on the stratum corneum, and in some other studies inter-individual differences overwhelms the racial difference. None of the studies comparatively analyzes the difference from the histopathological point of view. Here we report our harmonic generation microscopy study to analyze the difference of intrinsic aging between Caucasian and Asian skin from a histopathological point of view. As a result, the cellular and nuclear areas of basal cells in Caucasian subjects were found to increase at the same rate as the Asian subjects, ideal for scoring age. The maximum thickness of the viable epidermis, the dermal papilla (DP) volume per unit area and the depth of the DP zone in Caucasians were found to decrease at faster rates than those in Asians.

Slide-free imaging of hematoxylin-eosin stained whole-mount tissues using combined third-harmonic generation and three-photon fluorescence microscopy.

Intraoperative margin assessment of surgical tissues during cancer surgery is clinically important, especially in the case of tissue conserving surgery like Mohs micrographic surgery in which minimization of the surgical area is considered crucial. Frozen pathology is the gold standard of assessing excised tissues for signs of remaining cancerous lesions. The current protocol, however, is time-consuming and labor-intensive. Instead of the complex frozen sectioning, staining, and traditional white light microscopy imaging protocol, optically sectioned histopathological imaging of hematoxylin-eosin stained whole-mount skin tissues with a subfemtoliter resolution is demonstrated by using nonlinear microscopy in this study. With our proposed method, the reagents of staining and the contrast of imaging are fully consistent with the current clinical standard of frozen pathology, thus facilitating rapid intraoperative assessment of surgical tissues for future applications. Image: Slide-free nonlinear microscopy imaging of H&E stained whole-mount skin tissue showing the morphology of sweat glands.

Classification of established atopic dermatitis in children with the in vivo imaging methods.

Atopic dermatitis (AD) is a cutaneous disease resulting from a defective barrier and dysregulated immune response. The severity scoring of atopic dermatitis (SCORAD) is used to classify AD. Noninvasive imaging approaches supplementary to SCORAD were investigated. Cr:forsterite laser-based microscopy was employed to analyze endogenous third-harmonic generation (THG) and second-harmonic generation (SHG) signals from skin. Imaging parameters were compared between different AD severities. Three-dimensional reconstruction of imaged skin layers was performed. Finally, statistic models from quantitative imaging parameters were developed for predicting disease severity. Our data demonstrate that THG signal intensity of lesional skin in AD were significantly increased and was positively correlated with AD severity. Characteristic gray level co-occurrence matrix (GLCM) values were observed in more severe AD. In the 3D reconstruction video, individual dermal papilla and obvious fibrosis in the upper papillary dermis were easily identified. Our estimation models could predict the disease severity of AD patients with an accuracy of nearly 85%. The THG signal intensity and characteristic GLCM patterns are associated with AD severity and can serve as quantitative predictive parameters. Our imaging approach can be used to identify the histopathological changes of AD objectively, and to complement the SCORAD index, thus improving the accuracy of classifying AD severity.

High Sensitivity of T-Ray for Thrombus Sensing.

Atherosclerotic plaque rupture or erosion and subsequent development of platelet-containing thrombus formation is the fundamental cause of cardiovascular disease, which is the most common cause of death and disability worldwide. Here we show the high sensitivity of 200-270 GHz T-ray to distinguish thrombus formation at its early stage from uncoagulated blood. A clinical observational study was conducted to longitudinally monitor the T-ray absorption constant of ex-vivo human blood during the thrombus formation from 29 subjects. Compared with the control group (28 subjects) with uncoagulated blood samples, our analysis indicates the high sensitivity of 200-270 GHz T-Ray to detect thrombus with a low p-value < 10-5. Further analysis supports the significant role of platelet-activated thrombotic cascade, which modified the solvation dynamics of blood and occurred during the early coagulation stage, on the measured T-Ray absorption change. The ability to sense the thrombus formation at its early stage would hold promise for timely identification of patients at risk of various atherothrombotic disorders and save billions of lives.

Differentiating intratumoral melanocytes from Langerhans cells in nonmelanocytic pigmented skin tumors in vivo by label-free third-harmonic generation microscopy.

Morphology and distribution of melanocytes are critical imaging information for the diagnosis of melanocytic lesions. However, how to image intratumoral melanocytes noninvasively in pigmented skin tumors is seldom investigated. Third-harmonic generation (THG) is shown to be enhanced by melanin, whereas high accuracy has been demonstrated using THG microscopy for in vivo differential diagnosis of nonmelanocytic pigmented skin tumors. It is thus desirable to investigate if label-free THG microscopy was capable to in vivo identify intratumoral melanocytes. In this study, histopathological correlations of label-free THG images with the immunohistochemical images stained with human melanoma black (HMB)-45 and cluster of differentiation 1a (CD1a) were made. The correlation results indicated that the intratumoral THG-bright dendritic-cell-like signals were endogenously derived from melanocytes rather than Langerhans cells (LCs). The consistency between THG-bright dendritic-cell-like signals and HMB-45 melanocyte staining showed a kappa coefficient of 0.807, 84.6% sensitivity, and 95% specificity. In contrast, a kappa coefficient of −0.37, 21.7% sensitivity, and 30% specificity were noted between the THG-bright dendritic-cell-like signals and CD1a staining for LCs. Our study indicates the capability of noninvasive label-free THG microscopy to differentiate intratumoral melanocytes from LCs, which is not feasible in previous in vivo label-free clinical-imaging modalities.

A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae.

BACKGROUND: Defining a measure for regulatory similarity (RS) of two genes is an important step toward identifying co-regulated genes. To date, transcription factor binding sites (TFBSs) have been widely used to measure the RS of two genes because transcription factors (TFs) binding to TFBSs in promoters is the most crucial and well understood step in gene regulation. However, existing TFBS-based RS measures consider the relation of a TFBS to a gene as a Boolean (either 'presence' or 'absence') without utilizing the information of TFBS locations in promoters. RESULTS: Functional TFBSs of many TFs in yeast are known to have a strong positional preference to occur in a small region in the promoters. This biological knowledge prompts us to develop a novel RS measure that exploits the TFBS location information. The performances of different RS measures are evaluated by the fraction of gene pairs that are co-regulated (validated by literature evidence) by at least one common TF under different RS scores. The experimental results show that the proposed RS measure is the best co-regulation indicator among the six compared RS measures. In addition, the co-regulated genes identified by the proposed RS measure are also shown to be able to benefit three co-regulation-based applications: detecting gene co-function, gene co-expression and protein-protein interactions. CONCLUSIONS: The proposed RS measure provides a good indicator for gene co-regulation. Besides, its good performance reveals the importance of the location information in TFBS-based RS measures.